GgaINT0046946 @ galGal4
Intron Retention
Gene
ENSGALG00000011009 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr7:19357965-19359107:-
Coord C1 exon
chr7:19358966-19359107
Coord A exon
chr7:19358172-19358965
Coord C2 exon
chr7:19357965-19358171
Length
794 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
TATTATCTCTTTTTCCCCAGACA
3' ss Score
10.12
Exon sequences
Seq C1 exon
TCAATGTCCAGAAGGATATATATGTGTGAAAGCTGGTAGAAACCCCAACTATGGCTACACAAGTTTTGATACATTCAGTTGGGCATTCTTGTCACTGTTTCGATTGATGACTCAGGACTTTTGGGAGAATCTTTACCAGCTG
Seq A exon
GTGAGGACTTATTAAAATAAACAGCACCATCACCAATACCATTACTACATAGTATTTGCATAGTTCTTTTCATTCACATGTACCTGAGATCTTTGGGACACAAATCATCTTTTATTTCATATATATAAGCTCTCTAAAACAATAGGGGCCTTAGATTTCTGTGTGCTTCTTAAATACATAATAAGAAATAATTGTTAAGAATTATTGTTTCCTTTTCACAAATGAGTAAATGAACTTGTTAATGCTTCTTGCCCAAACATGTTGCAGACAGATGCTTGCTAAATTGATTTGCAGTCTAGTAGAGTTATATTGTCTTTGAGAAGGTTACACCTTGTCCCTGAAATACACACATCCTTAACCTGAAGGACTGTGATGTTGTGCAGGATGACATTTTGTATACTGCATTGGCTTTGTGGTACTGTAGTTTGAGTCTGATAAGACAAGGTAAGATACTGGCTAGTGGCCCCATTACTATTAAAGTAGTTTAAAGGCTATATTAAAAAGATATAATGGAGGCAGCAACTCCTGTAAGAGATTTTCATTGATAGGTGTTCTGAACTATTTAAACTACTGAATCATAGTCAGCTGTACCATAGCAGACACAGAACTTGGATTTTTACACATGTAGCTACGATGTAATACTATCTAGTTGTATGTGGAAAAAATAGCATAATCATCTTGTGATAAAAAAGAGAAAATTTACGATGTATTTCTAATCTATACCATAGATACCACAAGATTATATAACAGTGTGTAAAAGTCTTCTAAAAAGTGTATTATCTCTTTTTCCCCAG
Seq C2 exon
ACACTGCGTGCTGCTGGAAAAACATATATGATATTTTTTGTTTTGGTCATTTTCCTGGGCTCTTTCTACCTGATTAATTTGATCCTGGCTGTGGTTGCTATGGCCTATGAAGAACAGAATCAAGCAACCATGGAAGAAGCAGAACAGAAAGAAGCAGAATTTCAGCAAATGCTGGAACAACTGAAAAAGCAACAGGAAGAAGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011009:ENSGALT00000017933:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.203
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(17.5=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(11.6=44.9),PF143621=DUF4407=PU(39.3=79.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGAAGGATATATATGTGTGAAAGC
R:
CTGAGCTTCTTCCTGTTGCTT
Band lengths:
342-1136
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]